Tetraloop-like Geometries Could Form the Basis of the Catalytic
Activity of the Most Ancient Ribooligonucleotides

J 2015

Tetraloop-like Geometries Could Form the Basis of the Catalytic Activity of the Most Ancient Ribooligonucleotides

STADLBAUER, Petr; Jiří ŠPONER; Giovanna COSTANZO; Ernesto DI MAURO; Samanta PINO et al.

Základní údaje

Originální název

Tetraloop-like Geometries Could Form the Basis of the Catalytic Activity of the Most Ancient Ribooligonucleotides

Autoři

STADLBAUER, Petr; Jiří ŠPONER; Giovanna COSTANZO; Ernesto DI MAURO; Samanta PINO a Judit ŠPONEROVÁ

Vydání

Chemistry - A European Journal, WEINHEIM, WILEY-VCH, 2015, 0947-6539

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Německo

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.771

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/15:00082899

Organizační jednotka

Středoevropský technologický institut

Klíčová slova anglicky

catalysis; molecular dynamics; oligonucleotides; ribozymes; RNA

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 29. 3. 2016 15:18, Mgr. Eva Špillingová

Anotace

V originále

The origin of the catalytic activity of ancient oligonucleotides is a largely unexplored field of contemporary science. In the current work we use molecular dynamics simulations to investigate the plausibility of tetraloop-like overhang geometries to initiate transphosphorylation reactions that lead to ligation and terminal cleavage in simple, Watson-Crick (WC) complementary oligoC/oligoG sequences observed experimentally. We show a series of examples of known tetraloop architectures, which can be adopted by the unpaired overhangs of short oligonucleotide sequences for a sufficiently long time to enable chemical reactions that lead to simple ribozyme-like catalytic activity. Thus, our computations demonstrate that the role of non-WC interactions at the emergence of the most ancient catalytic oligonucleotides could be more significant than ever believed.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

Citovat

STADLBAUER, Petr; Jiří ŠPONER; Giovanna COSTANZO; Ernesto DI MAURO; Samanta PINO a Judit ŠPONEROVÁ. Tetraloop-like Geometries Could Form the Basis of the Catalytic Activity of the Most Ancient Ribooligonucleotides. Chemistry - A European Journal. WEINHEIM: WILEY-VCH, 2015, roč. 21, č. 9, s. 3596-3604. ISSN 0947-6539. Dostupné z: https://doi.org/10.1002/chem.201406140.

@article{1299594,
   author = {Stadlbauer, Petr and Šponer, Jiří and Costanzo, Giovanna and Di Mauro, Ernesto and Pino, Samanta and Šponerová, Judit},
   article_location = {WEINHEIM},
   article_number = {9},
   doi = {https://doi.org/10.1002/chem.201406140},
   keywords = {catalysis; molecular dynamics; oligonucleotides; ribozymes; RNA},
   language = {eng},
   issn = {0947-6539},
   journal = {Chemistry - A European Journal},
   title = {Tetraloop-like Geometries Could Form the Basis of the Catalytic Activity of the Most Ancient Ribooligonucleotides},
   url = {http://onlinelibrary.wiley.com/doi/10.1002/chem.201406140/epdf},
   volume = {21},
   year = {2015}
}

TY  - JOUR
ID  - 1299594
AU  - Stadlbauer, Petr - Šponer, Jiří - Costanzo, Giovanna - Di Mauro, Ernesto - Pino, Samanta - Šponerová, Judit
PY  - 2015
TI  - Tetraloop-like Geometries Could Form the Basis of the Catalytic Activity of the Most Ancient Ribooligonucleotides
JF  - Chemistry - A European Journal
VL  - 21
IS  - 9
SP  - 3596-3604
EP  - 3596-3604
PB  - WILEY-VCH
SN  - 09476539
KW  - catalysis
KW  - molecular dynamics
KW  - oligonucleotides
KW  - ribozymes
KW  - RNA
UR  - http://onlinelibrary.wiley.com/doi/10.1002/chem.201406140/epdf
L2  - http://onlinelibrary.wiley.com/doi/10.1002/chem.201406140/epdf
N2  - The origin of the catalytic activity of ancient oligonucleotides is a largely unexplored field of contemporary science. In the current work we use molecular dynamics simulations to investigate the plausibility of tetraloop-like overhang geometries to initiate transphosphorylation reactions that lead to ligation and terminal cleavage in simple, Watson-Crick (WC) complementary oligoC/oligoG sequences observed experimentally. We show a series of examples of known tetraloop architectures, which can be adopted by the unpaired overhangs of short oligonucleotide sequences for a sufficiently long time to enable chemical reactions that lead to simple ribozyme-like catalytic activity. Thus, our computations demonstrate that the role of non-WC interactions at the emergence of the most ancient catalytic oligonucleotides could be more significant than ever believed.
ER  -

STADLBAUER, Petr; Jiří ŠPONER; Giovanna COSTANZO; Ernesto DI MAURO; Samanta PINO a Judit ŠPONEROVÁ. Tetraloop-like Geometries Could Form the Basis of the Catalytic Activity of the Most Ancient Ribooligonucleotides. \textit{Chemistry - A European Journal}. WEINHEIM: WILEY-VCH, 2015, roč.~21, č.~9, s.~3596-3604. ISSN~0947-6539. Dostupné z: https://doi.org/10.1002/chem.201406140.

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